An employment judge has upheld a ruling that an SNP councillor’s belief in independence is similar to a religion.

Ministry of Defence (MoD) lawyers appealed the decision in a discrimination case brought by Nationalist Chris McEleny, but Judge Eccles has rejected the legal bid.

She wrote that it would not be “in the interests of justice” to reconsider her earlier judgement and noted the MoD had not provided any new evidence.

The row goes back to McEleny, the SNP group leader on Inverclyde council, announcing in 2016 that he would be running to become his party’s depute leader on a national level.

He was also an electrician at the MOD plant in Beith but, after the contest had begun, he was suspended and had his security clearance revoked.

In an interview with security officials, he was quizzed about his mental health, as well as his support for independence and opposition to Trident. He was also asked about social media posts in relation to Rangers.

Although he was reinstated months later, McEleny believed he had been targeted over his political views and took the MoD to an employment tribunal.

However, the case could only proceed if McEleny convinced a judge that his pro-independence stance amounted to a “philosophical” belief under equalities legislation, and therefore a “protected characteristic”.

In a historic case unrelated to the councillor, a judge had backed a staff member who argued that he had been made redundant on account of his belief in climate change. McEleny used this precedent, dubbed “Grainger”, at his tribunal.

Reflecting the legal tests set by Grainger, the councillor argued that his belief independence was “genuinely held” and “serious, cohesive and important”.

A summary of his case stated: “The claimant submitted that he was not claiming to believe that Scottish independence could improve the lives and economy of Scottish people. His belief that decisions regarding Scotland should be made by the people of Scotland regardless of the outcome will never change.”

In response, the MOD argued there was big difference between political opinion or affiliation, and a philosophical belief, adding that independence does not have a “similar status or cogency” to a religious belief”.

The UK Government department continued: “It [independence] does not impact on people in a general sense and provide a moral and ethical code by which people choose to live their lives.

“Regardless of its importance to the electorate of Scotland ... Scottish independence and the SNP have no substantial impact on the lives of citizens in for example Tanzania, Peru or India.”

In her original ruling, Judge Eccles backed McEleny: “He does not believe in Scottish independence because it will necessarily lead to improved economic and social conditions for people living in Scotland. It is a fundamental belief in the right of Scotland to national sovereignty.”

The judge continued: “I also do not accept that because Scottish independence might not impact on someone living in Tanzania ... or that Scottish independence is not of concern to a Tanzanian prevents the claimant’s belief from being philosophical in nature."

She added: “The claimant has persuaded me that his belief in Scottish independence has a sufficiently similar cogency to a religious belief as required by Justice Burton in Grainger to qualify as a philosophical belief.”

However, the MoD lodged an “application for reconsideration” and argued that the judge had “failed to correctly identify” McEleny’s belief in the context of Grainger.

It can now be revealed that Judge Eccles dismissed the appeal: “I am not persuaded that I misunderstood the claimant’s evidence about his belief or analysed a belief other than the one in relation to which he sought protection.”

She continued: “I was satisfied that his belief in Scottish independence could be ‘severed and considered separately’ from his belief in the social democratic values of the SNP.”

She also noted that the MoD sought a reconsideration on the grounds that McEleny’s view of independence “cannot possibly be shared” by the near 1.5 million people who Yes in the 2014 referendum.

The judge added: “I am not persuaded that it was necessary for me to find that each of the 1.5 million people who voted in favour of independence would, if asked, have articulated exactly the same belief as the claimant for his belief to be philosophical in nature.”

McEleny’s pro-independence views can now be relied on as a “protected” characteristic and a full hearing on the alleged discrimination will now take place.

He told this newspaper: “I very much welcome the decision and thank everyone for the support shown to date. Naturally, as I am sure people will understand, I will refrain from further comment until after the full conclusion of proceedings.”

The MOD did not offer comment.